[Chimera-users] 3D dashed lines

Greg Couch gregc at cgl.ucsf.edu
Mon Nov 29 17:31:04 PST 2010

For raytraced output, dashed lines are converted into multiple tiny 
cylinders, but there is a bug in the algorithm where it doesn't take 
into account the current scale factor, so you might end up with too many 

A temporary workaround is when saving a raytraced image to first change 
the POV-ray options to save the input files, then abort the raytracing 
and edit the image.pov file and change the second-to-the-last argument 
to the Dashes macro to the number of dashes you want and then run povray 
by hand:

     povray +Iimage.pov +Oimage.png image.ini

If povray isn't on your path, then you will need to give the full path.  
And if you use chimera's povray on Linux and Mac OS X, you need set 
LD_LIBRARY_PATH, ie., if CHIMERA is the top of the chimera hierarchy, then:

     LD_LIBRARY_PATH=CHIMERA/lib CHIMERA/bin/povray +Iimage.pov 
+Oimage.png image.ini

I'll try to get a fix into the daily builds soon.


On 11/28/2010 09:35 AM, Elaine Meng wrote:
> Hi Sundar,
> In the "structure analysis and comparison" tutorial images, the
> pseudobonds are flat lines, but I can see why you might think they
> were 3D dots or dashes: the dashed line is fairly thick, and sometimes
> the atoms on the ends are small balls.
> Regards,
> Elaine
> On Nov 27, 2010, at 6:55 PM, M Sundaramoorthy wrote:
>> Hi Elaine,
>> Thanks for your prompt reply. Perhaps, I imagined dotted stick in
>> the image of 2zcp active site in Analysis/Comparison tutorial. I'll
>> just stick to what is available now.
>> On the Side View panel, I found extremely faint grey square/lines
>> and now my eyes are trained to find them.
>> Regards,
>> Sundar
>> On Sat, Nov 27, 2010 at 3:47 PM, Elaine Meng<meng at cgl.ucsf.edu>
>> wrote:
>> Hi Sundar,
>> Currently there is no dashed or dotted stick option for pseudobonds
>> in the interactive view, sorry.  I don't know which tutorial image
>> you mean -- I made the tutorials in the User's Guide and I'm pretty
>> sure they don't have any such images.
>> I can think of one way to make dotted or dashed stick pseudobonds in
>> a static image from Chimera, but that is with the "neon" command,
>> which is not available on Windows.
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html>
>> Raytracing with Povray from Chimera will make a static image with
>> solid stick pseudobond even when it is shown as a line in the
>> interactive view, but even if the line is dashed or dotted, the
>> stick is continuous (unfortunately).  At least, that's what happened
>> just now when I tried it in recent builds of both version 1.5 and 1.6.
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html>
>> I can't answer the Side View part, but it might be a graphics driver
>> issue -- you could try updating your graphics driver.
>> Regards,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Nov 27, 2010, at 8:59 AM, M Sundaramoorthy wrote:
>>> I like to show pseudobonds (H-bonds, metal coordinations and
>> distances) as solid dotted or dashed lines.
>>> To draw dashed/dotted line I can choose dashed line style in the
>> Pseduobond attributes panel. But it works only with bond style
>> 'wire' not with 'stick'. It can essentially draws flat lines. How do
>> I show 3D dashed/dotted lines? Some images in the tutorial do have
>> such lines represented as dotted (spheres) lines.
>>> Another problem I have is that the Side View panel shows the image
>> but does not show the eye (the small square) and the clipping planes
>> (vertical lines). I am using Chimera 1.5rc in Windows Vista.
>>> Thanks
>>> Sundar
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